目的利用计算机预测结核分枝杆菌PPE家族蛋白MHC-II类分子限制性CD4+T细胞泛宿主表位,并利用γ干扰素释放实验进行体外验证。方法利用网上数据库提取PPE家族全部蛋白序列。使用生物信息学软件包括Signal P4.1,Secretome P 2.0,DAS和Net ...目的利用计算机预测结核分枝杆菌PPE家族蛋白MHC-II类分子限制性CD4+T细胞泛宿主表位,并利用γ干扰素释放实验进行体外验证。方法利用网上数据库提取PPE家族全部蛋白序列。使用生物信息学软件包括Signal P4.1,Secretome P 2.0,DAS和Net MHCII2.2等分析工具预测、筛选出MHC-II类分子限制性CD4+T细胞泛宿主表位。最后利用γ干扰素释放实验进行合成肽段的体外实验验证其刺激激活CD4+T细胞的能力。结果发现了34个泛宿主表位多肽,其中21个来自于PPE8蛋白,其余来自于PPE12、PPE21和PPE62蛋白。γ干扰素释放实验并未发现预测出的泛宿主表位多肽可刺激大量的CD4+T淋巴细胞产生IFN-γ的分泌,但来自于PPE8蛋白的两个泛宿主表位多肽可刺激少量的CD4+T淋巴细胞产生反应。结论这些计算机预测出来的泛宿主表位多肽,尤其是来自PPE8蛋白的泛宿主表位多肽,可能是下一步亚单位疫苗或诊断性标志物的重要候选抗原。但仍需进一步扩大样本量进行验证。展开更多
African swine fever virus(ASFV)infection poses enormous threats and challenges to the global pig industry;however,no effective vaccine is available against ASFV,attributing to the huge viral genome(approximately189 kb...African swine fever virus(ASFV)infection poses enormous threats and challenges to the global pig industry;however,no effective vaccine is available against ASFV,attributing to the huge viral genome(approximately189 kb)and numerous encoding products(>150 genes)due to the limited understanding on the molecular mechanisms of viral pathogenesis.Elucidating the host-factor/viral-protein interaction network will reveal new targets for developing novel antiviral therapies.Using proteomic analysis,we identified 255 cellular proteins that interact with the ASFV-encoded pE301R protein when transiently expressed in HEK293T cells.Gene ontology(GO)annotation,Kyoto Encyclopedia of Genes and Genomes(KEGG)database enrichment,and protein-protein interaction(PPI)network analyses revealed that pE301R-interacting host proteins are potentially involved in various biological processes,including protein translation and folding,response to stimulation,and mitochondrial transmembrane transport.The interactions of two putative cellular proteins(apoptosis inducing factor mitochondria associated 1(AIFM1)and vimentin(VIM))with pE301R-apoptosis inducing factor have been verified by co-immunoprecipitation.Our study revealed the inhibitory role of pE301R in interferon(IFN)induction that involves VIM sequestration by pE301R,identified interactions between ASFV pE301R and cellular proteins,and predicted the potential function of pE301R and its associated biological processes,providing valuable information to enhance our understanding of viral protein function,pathogenesis,and potential candidates for the prevention and control of ASFV infection.展开更多
Mycobacterium is a genus of bacteria with over a hundred non-pathogenic and pathogenic species, best recognized for certain members known to cause diseases such as tuberculosis and leprosy. Two novel protein families ...Mycobacterium is a genus of bacteria with over a hundred non-pathogenic and pathogenic species, best recognized for certain members known to cause diseases such as tuberculosis and leprosy. Two novel protein families important in the pathogenesis of Mycobacterium species are the PE and PPE families. These two protein families affect the antigenic profiles, disturbing host immunity. To better understand the origin and evolution of these gene families and the differences in their composition between pathogenic and non-pathogenic strains, several bioinformatic analyses were conducted both among Mycobacterium and closely related species that contain PE35 and PPE68 gene homologs. The methods included protein homology searches (BLASTP), horizontal gene transfer analysis (IslandViewer), phylogenetic analysis, gene cluster analysis and structural and functional constraints. Results revealed that PE and PPE gene homologs were not only limited to Mycobacterium, but also existed in three other non-mycobacterial genera, Rhodococcus, Tsukamurella and Segniliparus, and were possibly initially acquired from non-mycobacterial microorganisms by multiple horizontal gene transfers. Results also demonstrated that PE and PPE genes were more diverse and more rapidly evolving in pathogenic Mycobacterium as compared with non-pathogenic Mycobacterium and other non-mycobacterial species. These findings possibly shed light on the diverse functions and origins of the PE/PPE proteins among these organisms.展开更多
文摘目的利用计算机预测结核分枝杆菌PPE家族蛋白MHC-II类分子限制性CD4+T细胞泛宿主表位,并利用γ干扰素释放实验进行体外验证。方法利用网上数据库提取PPE家族全部蛋白序列。使用生物信息学软件包括Signal P4.1,Secretome P 2.0,DAS和Net MHCII2.2等分析工具预测、筛选出MHC-II类分子限制性CD4+T细胞泛宿主表位。最后利用γ干扰素释放实验进行合成肽段的体外实验验证其刺激激活CD4+T细胞的能力。结果发现了34个泛宿主表位多肽,其中21个来自于PPE8蛋白,其余来自于PPE12、PPE21和PPE62蛋白。γ干扰素释放实验并未发现预测出的泛宿主表位多肽可刺激大量的CD4+T淋巴细胞产生IFN-γ的分泌,但来自于PPE8蛋白的两个泛宿主表位多肽可刺激少量的CD4+T淋巴细胞产生反应。结论这些计算机预测出来的泛宿主表位多肽,尤其是来自PPE8蛋白的泛宿主表位多肽,可能是下一步亚单位疫苗或诊断性标志物的重要候选抗原。但仍需进一步扩大样本量进行验证。
基金supported by the National Key R&D Program of China (2019YFA0905700,2018YFA0900400)Natural Science Foundation of China (31900147,32170038,32270088,M-0348 and 32161133013)+2 种基金the 111 Project (B16030)a Sino-German Helmholtz International Lab grantsupported by US National Institutes of Health grant 1R01CA251698-01 and CPRIT grants RP180349 and RP190077.
文摘African swine fever virus(ASFV)infection poses enormous threats and challenges to the global pig industry;however,no effective vaccine is available against ASFV,attributing to the huge viral genome(approximately189 kb)and numerous encoding products(>150 genes)due to the limited understanding on the molecular mechanisms of viral pathogenesis.Elucidating the host-factor/viral-protein interaction network will reveal new targets for developing novel antiviral therapies.Using proteomic analysis,we identified 255 cellular proteins that interact with the ASFV-encoded pE301R protein when transiently expressed in HEK293T cells.Gene ontology(GO)annotation,Kyoto Encyclopedia of Genes and Genomes(KEGG)database enrichment,and protein-protein interaction(PPI)network analyses revealed that pE301R-interacting host proteins are potentially involved in various biological processes,including protein translation and folding,response to stimulation,and mitochondrial transmembrane transport.The interactions of two putative cellular proteins(apoptosis inducing factor mitochondria associated 1(AIFM1)and vimentin(VIM))with pE301R-apoptosis inducing factor have been verified by co-immunoprecipitation.Our study revealed the inhibitory role of pE301R in interferon(IFN)induction that involves VIM sequestration by pE301R,identified interactions between ASFV pE301R and cellular proteins,and predicted the potential function of pE301R and its associated biological processes,providing valuable information to enhance our understanding of viral protein function,pathogenesis,and potential candidates for the prevention and control of ASFV infection.
文摘Mycobacterium is a genus of bacteria with over a hundred non-pathogenic and pathogenic species, best recognized for certain members known to cause diseases such as tuberculosis and leprosy. Two novel protein families important in the pathogenesis of Mycobacterium species are the PE and PPE families. These two protein families affect the antigenic profiles, disturbing host immunity. To better understand the origin and evolution of these gene families and the differences in their composition between pathogenic and non-pathogenic strains, several bioinformatic analyses were conducted both among Mycobacterium and closely related species that contain PE35 and PPE68 gene homologs. The methods included protein homology searches (BLASTP), horizontal gene transfer analysis (IslandViewer), phylogenetic analysis, gene cluster analysis and structural and functional constraints. Results revealed that PE and PPE gene homologs were not only limited to Mycobacterium, but also existed in three other non-mycobacterial genera, Rhodococcus, Tsukamurella and Segniliparus, and were possibly initially acquired from non-mycobacterial microorganisms by multiple horizontal gene transfers. Results also demonstrated that PE and PPE genes were more diverse and more rapidly evolving in pathogenic Mycobacterium as compared with non-pathogenic Mycobacterium and other non-mycobacterial species. These findings possibly shed light on the diverse functions and origins of the PE/PPE proteins among these organisms.
